4x7e - Revision history

OCA at 10:47, 10 January 2024

2024-01-10T10:47:33Z

←Older revision		Revision as of 10:47, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus Norovirus] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus Norovirus] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X7E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.11Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [https://pdbe.org/4x7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [https://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [https://pdbe.org/4x7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [https://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:16, 12 April 2023

2023-04-12T21:16:04Z

←Older revision		Revision as of 21:16, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4x7e' size='340' side='right'caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>		<StructureSection load='4x7e' size='340' side='right'caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alpaca Alpaca~~] and [~~http~~://en.wikipedia.org/wiki/~~Norovirus Norovirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus Norovirus] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X7E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [~~http~~://pdbe.org/4x7e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [https://pdbe.org/4x7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [https://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5F4T5_9CALI Q5F4T5_9CALI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpaca]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Norovirus]]		[[Category: Norovirus]]
-	[[Category: ~~Hansman, G H~~]]	+	[[Category: Vicugna pacos]]
-	[[Category: ~~Koromyslova, A D~~]]	+	[[Category: Hansman GH]]
-	[[Category: ~~Nanobody]]~~	+	[[Category: Koromyslova AD]]
-	~~[[Category: Protruding domain]]~~	+
-	~~[[Category: Vhh domain]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 06:59, 29 May 2019

2019-05-29T06:59:55Z

←Older revision		Revision as of 06:59, 29 May 2019
Line 1:		Line 1:

	==Crystal structure of norovirus GII.10 P domain in complex with Nano-85==		==Crystal structure of norovirus GII.10 P domain in complex with Nano-85==
-	<StructureSection load='4x7e' size='340' side='right' caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>	+	<StructureSection load='4x7e' size='340' side='right'caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Norovirus Norovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://pdbe.org/4x7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://pdbe.org/4x7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4x7e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x7e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alpaca]]
		+	[[Category: Large Structures]]
		+	[[Category: Norovirus]]
	[[Category: Hansman, G H]]		[[Category: Hansman, G H]]
	[[Category: Koromyslova, A D]]		[[Category: Koromyslova, A D]]
	[[Category: Nanobody]]		[[Category: Nanobody]]
-	[[Category: Norovirus]]
	[[Category: Protruding domain]]		[[Category: Protruding domain]]
	[[Category: Vhh domain]]		[[Category: Vhh domain]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 00:15, 26 January 2017

2017-01-26T00:15:32Z

←Older revision		Revision as of 00:15, 26 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of norovirus GII.10 P domain in complex with Nano-85==		==Crystal structure of norovirus GII.10 P domain in complex with Nano-85==
	<StructureSection load='4x7e' size='340' side='right' caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>		<StructureSection load='4x7e' size='340' side='right' caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://pdbe.org/4x7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x7e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4x7e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:39, 14 January 2015

2015-01-14T07:39:27Z

←Older revision		Revision as of 07:39, 14 January 2015
Line 6:		Line 6:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human noroviruses are icosahedral single-stranded RNA viruses. The capsid protein is divided into shell (S) and protruding (P) domains, which are connected by a flexible hinge region. There are numerous genetically and antigenically distinct noroviruses and the dominant strains evolve every other year. Vaccine and antiviral development is hampered by the difficulties in growing human norovirus in cell culture and the continually evolving strains. Here, we show the X-ray crystal structures of human norovirus P domains in complex with two different Nanobodies. One Nanobody, Nano-85, was broadly reactive, while the other, Nano-25, was strain specific. We showed that both Nanobodies bound to the lower region on the P domain and had nanomolar affinities. The Nano-85 binding site mainly compromised of highly conserved amino acids among the genetically distinct genogroup II noroviruses. Several of the conserved residues were also recognized by a broadly reactive monoclonal antibody, which suggested this region contained a dominant epitope. Superposition of the P domain Nanobody complex structures into a cryo-EM particle structure revealed that both Nanobodies bound at occluded sites on the particles. The flexible hinge region, which contained approximately 10-12 amino acids, likely permitted a certain degree of P domain movement on the particles in order to accommodate the Nanobodies. Interestingly, the Nano-85 binding interaction with intact particles caused the particles to disassemble in vitro. Altogether, these results suggested that the highly conserved Nano-85 binding epitope contained a trigger mechanism for particle disassembly. Principally, this epitope represents a potential site of norovirus vulnerability. IMPORTANCE: We characterized two different Nanobodies (Nano-85 and Nano-25) that bind to human noroviruses. Both Nanobodies bound with high affinities to the lower region of the P domain, which was occluded on intact particles. Nano-25 was specific for GII.10, whereas Nano-85 bound several different GII genotypes, including GII.4, GII.10, and GII.12. We showed that Nano-85 was able to detect norovirus virions in clinical stool specimens using a sandwich ELISA. Importantly, we found that Nano-85 binding to intact particles caused the particles to disassemble. We believe that with further testing, Nano-85 will not only work as a diagnostic reagent in norovirus detection systems, but could also function as a broadly reactive GII norovirus antiviral.
		+
		+	Nanobody binding to a conserved epitope promoted human norovirus particle disassembly.,Koromyslova AD, Hansman GS J Virol. 2014 Dec 17. pii: JVI.03176-14. PMID:25520510<ref>PMID:25520510</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:56, 31 December 2014

2014-12-31T14:56:49Z

←Older revision		Revision as of 14:56, 31 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of norovirus GII.10 P domain in complex with Nano-85==
-		+	<StructureSection load='4x7e' size='340' side='right' caption='[[4x7e]], [[Resolution\|resolution]] 2.11Å' scene=''>
-	~~The entry~~ 4x7e is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4x7e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X7E FirstGlance]. <br>
-	~~Authors~~: ~~Hansman, G~~.H.~~, Koromyslova, A~~.D.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x7e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x7e RCSB], [http://www.ebi.ac.uk/pdbsum/4x7e PDBsum]</span></td></tr>
-	~~Description~~:	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
-	[[Category: Hansman, G.H]]	+	</StructureSection>
-	[[Category: Koromyslova, A.D]]	+	[[Category: Hansman, G H]]
		+	[[Category: Koromyslova, A D]]
		+	[[Category: Nanobody]]
		+	[[Category: Norovirus]]
		+	[[Category: Protruding domain]]
		+	[[Category: Vhh domain]]
		+	[[Category: Viral protein]]

OCA at 20:35, 24 December 2014

2014-12-24T20:35:52Z

←Older revision		Revision as of 20:35, 24 December 2014
Line 5:		Line 5:
	Authors: Hansman, G.H., Koromyslova, A.D.		Authors: Hansman, G.H., Koromyslova, A.D.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Hansman, G.H]]
		+	[[Category: Koromyslova, A.D]]

OCA at 10:00, 24 December 2014

2014-12-24T10:00:35Z

←Older revision		Revision as of 10:00, 24 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4x7e is ON HOLD	+	The entry 4x7e is ON HOLD until Paper Publication

	Authors: Hansman, G.H., Koromyslova, A.D.		Authors: Hansman, G.H., Koromyslova, A.D.

	Description:		Description:

OCA: Protected "4x7e" [edit=sysop:move=sysop]

2014-12-17T11:45:18Z

Protected "4x7e" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:45, 17 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x7e is ON HOLD Authors: Hansman, G.H., Koromyslova, A.D. Description:

2014-12-17T11:45:17Z

New page: '''Unreleased structure''' The entry 4x7e is ON HOLD Authors: Hansman, G.H., Koromyslova, A.D. Description:

New page

'''Unreleased structure'''

The entry 4x7e is ON HOLD

Authors: Hansman, G.H., Koromyslova, A.D.

Description: